Proteomics is the study of protein expression at a global level for a specific cell type, tissue or organ. A primary objective of Proteomics is the identification of differentially expressed proteins after experimental treatment, environmental contaminant exposure or in human disease. Understanding global changes in gene expression at the protein level will be a useful tool for experimental biology, can implicate new targets or pathways for therapeutics, and will provide new markers for environmental toxicology. Proteomics is accomplished by combining protein separation like 2D gel electrophoresis and identification technologies such as mass spectrometry (MS) in a sequential and automated fashion. It is also important to use complementry power of expression technologies like proteomics and cDNA microarray inresearch problem areas. Several such proteomics studies have been completed. In one study, effects of acute dioxin treatment on protein expression in liver have revealed changes in the NFkB pathway involving altered distribution of activating kinases and inhibitory proteins. In another study, subacute treatment with the metabolic enzyme inducer, phenobarbital, have shown alterations in over 60 proteins by proteomic analysis using a subcellular fractionation strategy. When compared with cDNA microarray analysis of the same tissue, many of the same changes in gene expression occurred at the message and protein level while important differences, particularly in nuclear proteins, were noted by proteomics. In other work with arensic transformed cells, results showed alterations in growth control genes at the mRNA and protein level, particularly indicating a relationship with c-myc overexpression and aresenic expsoure with increased cell proliferation. These collective studies demonstrate the value of global protein analysis in pointing to key pathways altered in response to toxicant exposure as well as the value of performing parallel cDNA microarray analysis.